JAL-2527 move default colours for applet / application out of gui.Preferences so...

[jalview.git] / src / jalview / gui / OverviewCanvas.java

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index e49fd19..64bf15c 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -21,11 +21,14 @@
 package jalview.gui;
 
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.event.ActionEvent;
@@ -37,7 +40,7 @@ import javax.swing.Timer;
 
 public class OverviewCanvas extends JComponent
 {
-  private static final long RUNNING_TIME = 2000;
+  private static final long RUNNING_TIME = 1000;
 
   private static final int SPEED = 40;
 
@@ -49,6 +52,8 @@ public class OverviewCanvas extends JComponent
 
   private volatile boolean updaterunning = false;
 
+  private boolean dispose = false;
+
   private BufferedImage miniMe;
 
   private BufferedImage lastMiniMe = null;
@@ -67,6 +72,9 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewportI av;
 
+
+  private OverviewResColourFinder cf;
+
   private float alpha = 0f;
 
   private long startTime = -1;
@@ -84,9 +92,15 @@ public class OverviewCanvas extends JComponent
 
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
-    sr.forOverview = true;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
 
+    boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
+    Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+    Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+
     setSize(od.getWidth(), od.getHeight());
 
     timer = new Timer(SPEED, new ActionListener()
@@ -118,6 +132,7 @@ public class OverviewCanvas extends JComponent
         }
       }
     });
+
   }
 
   /**
@@ -168,9 +183,6 @@ public class OverviewCanvas extends JComponent
   public void draw(boolean showSequenceFeatures, boolean showAnnotation,
           FeatureRenderer transferRenderer)
   {
-    // System.out.println(this.getHeight());
-    // setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
     miniMe = null;
     veryLastMiniMe = lastMiniMe;
 
@@ -179,8 +191,13 @@ public class OverviewCanvas extends JComponent
       fr.transferSettings(transferRenderer);
     }
 
-    or = new OverviewRenderer(sr, fr, od);
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
+    or = new OverviewRenderer(fr, od, av.getAlignment(),
+            av.getResidueShading(), cf);
+
     or.addPropertyChangeListener(progressPanel);
+
     miniMe = or.draw(od.getRows(av.getAlignment()),
             od.getColumns(av.getAlignment()));
 
@@ -197,10 +214,14 @@ public class OverviewCanvas extends JComponent
     System.gc();
 
     or.removePropertyChangeListener(progressPanel);
+    or = null;
     if (restart)
     {
       restart = false;
-      draw(showSequenceFeatures, showAnnotation, transferRenderer);
+      if (!dispose)
+      {
+        draw(showSequenceFeatures, showAnnotation, transferRenderer);
+      }
     }
     else
     {
@@ -214,7 +235,6 @@ public class OverviewCanvas extends JComponent
   @Override
   public void paintComponent(Graphics g)
   {
-
     if (restart)
     {
       if (lastMiniMe == null)
@@ -231,12 +251,12 @@ public class OverviewCanvas extends JComponent
     }
     else if (lastMiniMe != null)
     {
+      // is this a resize?
       if ((getWidth() > 0) && (getHeight() > 0)
               && ((getWidth() != od.getWidth())
                       || (getHeight() != od.getHeight())))
       {
-        // scale the alignment and annotation separately *** if there is
-        // annotation ***
+        // if there is annotation, scale the alignment and annotation separately
         if (od.getGraphHeight() > 0)
         {
           BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
@@ -263,8 +283,6 @@ public class OverviewCanvas extends JComponent
         }
         else
         {
-          System.out.println("Resetting height from/to: " + od.getHeight()
-                  + " " + getHeight());
           od.setWidth(getWidth());
           od.setHeight(getHeight());
         }
@@ -276,7 +294,7 @@ public class OverviewCanvas extends JComponent
         od.setBoxPosition(av.getAlignment().getHiddenSequences(),
                 av.getAlignment().getHiddenColumns());
       }
-      else
+      else // not a resize
       {
         if (alpha != 0) // this is a timer triggered dissolve
         {
@@ -292,24 +310,29 @@ public class OverviewCanvas extends JComponent
 
           g2d.dispose();
         }
-        /*       else if (lastMiniMe != miniMe)
-        {
-          g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
-          g.setColor(TRANS_GREY);
-          g.fillRect(0, 0, getWidth(), getHeight());
-        }*/
         else
         {
           // fall back to normal behaviour
           g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
         }
-
       }
-
     }
 
     // draw the box
     g.setColor(Color.red);
     od.drawBox(g);
   }
+
+  public void dispose()
+  {
+    dispose = true;
+    synchronized (this)
+    {
+      restart = true;
+      if (or != null)
+      {
+        or.setRedraw(true);
+      }
+    }
+  }
 }